Question: Data format to produces a heatmap like this
1
gravatar for prp291
2.9 years ago by
prp29150
United States
prp29150 wrote:

Hi,

My question is simple. I am just not just that how to arrange my data matrix to produces a heatmap to show a disticnt band in each tissue (preferential expression) like Figure 4 of this article

 

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064058

 

Thanks

 

 

heatmap rna-seq R • 1.2k views
ADD COMMENTlink modified 2.9 years ago by Alternative210 • written 2.9 years ago by prp29150
1

Try this for GUI....very good

http://www.hiv.lanl.gov/content/sequence/HEATMAP/heatmap_mainpage.html

ADD REPLYlink written 2.9 years ago by kumar.vinod81280
0
gravatar for Alternative
2.9 years ago by
Alternative210
Alternative210 wrote:

Try to play with different clustering algorithms (i.e ward, ...) and different scales and scale colors when drawing your heatmap. In their methods they say that they used heatmap.2 (R package).

Hint: by limiting the scale, you avoid outliers from messing up with your scale and heatmap colors.

 

ADD COMMENTlink written 2.9 years ago by Alternative210

I tried different clustering algorithm but none of them seems to work for me. Thanks though

ADD REPLYlink written 2.9 years ago by prp29150

Do you know that you have such a structure for your data ? If you know which tissue each row corresponds to, you can just reorder your matrix to group the rows by tissue. If there is a structure corresponding to tissues, it should become apparent (possibly with the proper scaling as Pierre suggested).

ADD REPLYlink written 2.9 years ago by Jean-Karim Heriche16k
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